Establishment of LCMS Based Platform for Discovery of Quorum Sensing Inhibitors: Signal Detection in Pseudomonas aeruginosa PAO1

Capsaicin from chili peppers and its analogues and their valued applications: An updated literature review

Chili peppers are widely sought after by consumers for not only their color, flavor, and nutritional properties but also their main component (capsaicin) various biological activities in diverse fields. Capsaicin (trans-8-methyl-N-vanillyl-6-nonenamide), the compound primarily responsible for the spicy flavor of peppers, remains a hot topic in the scientific community and shows the vast potential in various applications. Although many reviews focus comprehensively on capsaicin, most articles are limited to the medical field of capsaicin. This review provides an overview briefly of the capsaicin and its analogues in the fields of food, medicine and with a particular emphasis on their applications in agriculture and livestock farming. Overall, we aims is to expand the broad spectrum of applications for capsaicin and its analogues and explore their potential biological mechanisms. Finally, the challenges of capsaicin and future development prospects were discussed and proposed.

A Label-Free Approach for Relative Spatial Quantitation of c-di-GMP in Microbial Biofilms

Microbial biofilms represent an important lifestyle for bacteria and are dynamic three-dimensional structures. Cyclic dimeric guanosine monophosphate (c-di-GMP) is a ubiquitous signaling molecule that is known to be tightly regulated with biofilm processes. While measurements of global levels of c-di-GMP have proven valuable toward understanding the genetic control of c-di-GMP production, there is a need for tools to observe the local changes of c-di-GMP production in biofilm processes. We have developed a label-free method for the direct detection of c-di-GMP in microbial colony biofilms using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). We applied this method to the enteric pathogen Vibrio cholerae, the marine symbiont V. fischeri, and the opportunistic pathogen Pseudomonas aeruginosa PA14 and detected spatial and temporal changes in c-di-GMP signal that accompanied genetic alterations in factors that synthesize and degrade the compound. We further demonstrated how this method can be simultaneously applied to detect additional metabolites of interest from a single sample.

A comprehensive review of genomics, transcriptomics, proteomics, and metabolomic insights into the differentiation of Pseudomonas aeruginosa from the planktonic to biofilm state: A multi-omics approach

Biofilm formation by Pseudomonas aeruginosa is primarily responsible for chronic wound and lung infections in humans. These infections are persistent owing to the biofilm's high tolerance to antimicrobials and constantly changing environmental factors. Understanding the mechanism governing biofilm formation can help to develop therapeutics explicitly directed against the molecular markers responsible for this process. After numerous years of research, many genes responsible for both in vitro and in vivo biofilm development remain unidentified. However, there is no "all in one" complete in vivo or in vitro biofilm model. Recent findings imply that the shift from planktonic bacteria to biofilms is a complicated and interrelated differentiation process. Research on the applications of omics technologies in P. aeruginosa biofilm development is ongoing, and these approaches hold great promise for expanding our knowledge of the mechanisms of biofilm formation. This review discusses the different factors that affect biofilm formation and compares P. aeruginosa biofilm formation using the omics approaches targeting essential biological macromolecules, such as DNA, RNA, Protein, and metabolome. Furthermore, we have outlined the application of currently available omics tools, such as genomics, proteomics, metabolomics, transcriptomics, and integrated multi-omics methodologies, to understand the differential gene expression (biofilm vs. planktonic bacteria) of P. aeruginosa biofilms.

High-Throughput, Quantitative Screening of Quorum-Sensing Inhibitors Based on a Bacterial Biosensor

Quorum sensing (QS) is a cell-cell communication mechanism by which bacteria synchronize social behaviors such as biofilm formation and virulence factor secretion by producing and sensing small molecular signals. Quorum quenching (QQ) by degrading signals or blocking signal transmissions has become a promising strategy for disrupting QS and preventing bacterial infection and biofilm formation. However, studies of high-throughput screening and identification approaches for quorum-sensing inhibitors (QSIs) are still inadequate. In this work, we developed a sensitive, high-throughput approach for screening QSIs based on the bacterial biosensor strain Agrobacterium tumefaciens N5 (pBA7P), which contains a traG gene promoter induced by QS signals fused with a promoterless β-lactamase gene reporter. Using this approach, we identified 31 QQ bacteria from ∼2000 soil bacterial isolates, some belonging to the genera Bosea, Cupriavidus, and Flavobacterium that have not been reported previously as QQ bacteria. We also identified four QS inhibitory compounds and one QS signal analogue from ∼5000 small-molecule compounds, which profoundly affected the expression of QS-regulated genes and phenotypes of the pathogenic bacteria. This high-throughput screening system is effective and sensitive for screening of both QQ microbes and small molecules, enabling the discovery of a wide variety of biocompatible compounds.

A label-free approach for relative spatial quantitation of c-di-GMP in microbial biofilms

Microbial biofilms represent an important lifestyle for bacteria and are dynamic three dimensional structures. Cyclic dimeric guanosine monophosphate (c-di-GMP) is a ubiquitous signaling molecule that is known to be tightly regulated with biofilm processes. While measurements of global levels of c-di-GMP have proven valuable towards understanding the genetic control of c-di-GMP production, there is a need for tools to observe the local changes of c-di-GMP production in biofilm processes. We have developed a label-free method for the direct detection of c-di-GMP in microbial colony biofilms using matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI). We applied this method to the enteric pathogen Vibrio cholerae, the marine symbiont V. fischeri, and the opportunistic pathogen Pseudomonas aeruginosa PA14 and detected spatial and temporal changes in c-di-GMP signal that accompanied genetic alterations in factors that synthesize and degrade the compound. We further demonstrated how this method can be simultaneously applied to detect additional metabolites of interest in a single experiment.

Antimicrobial Properties of Capsaicin: Available Data and Future Research Perspectives

Capsaicin is a phytochemical derived from plants of the genus Capsicum and subject of intensive phytochemical research due to its numerous physiological and therapeutical effects, including its important antimicrobial properties. Depending on the concentration and the strain of the bacterium, capsaicin can exert either bacteriostatic or even bactericidal effects against a wide range of both Gram-positive and Gram-negative bacteria, while in certain cases it can reduce their pathogenicity by a variety of mechanisms such as mitigating the release of toxins or inhibiting biofilm formation. Likewise, capsaicin has been shown to be effective against fungal pathogens, particularly Candida spp., where it once again interferes with biofilm formation. The parasites Toxoplasma gondi and Trypanosoma cruzi have been found to be susceptible to the action of this compound too while there are also viruses whose invasiveness is significantly dampened by it. Among the most encouraging findings are the prospects for future development, especially using new formulations and drug delivery mechanisms. Finally, the influence of capsaicin in somatostatin and substance P secretion and action, offers an interesting array of possibilities given that these physiologically secreted compounds modulate inflammation and immune response to a significant extent.

Plant Protection Mediated Through an Array of Metabolites Produced by Pantoea dispersa Isolated from Pitcher Plant

In the study, the bacterial isolate NhPB54 purified from the pitcher of Nepenthes plant was observed to have activity against Pythium aphanidermatum by dual culture and well diffusion. Hence, it was subjected to 16S rDNA sequencing and BLAST analysis, where the NhPB54 was found to have 100% identity to Pantoea dispersa. Upon screening for the plant beneficial properties, Pantoea dispersa NhPB54 was found to be positive for phosphate, potassium and zinc solubilization, nitrogen fixation, indole-3-acetic acid, ammonia, 1-aminocyclopropane-1-carboxylate deaminase, biofilm and biosurfactant production. Further to this, Solanum lycopersicum seedlings primed with P. dispersa NhPB54 were studied for the improved plant growth and disease protection. Here, the seedlings pre-treated with the NhPB54 culture supernatant were found to have enhanced plant growth and protection from damping off and fruit rot caused by P. aphanidermatum. From the LC-QTOF-MS/MS and GC MS analysis, P. dispersa NhPB54 was found to produce a blend of chemicals including 1-hydroxyphenazine, surfactin, and other bioactive metabolites with the likely basis of its observed antifungal and plant growth-promoting properties. From the results of the study, plants with unique adaptations can expect to harbor microbial candidates with beneficial applications.

Cell division factor ZapE regulates Pseudomonas aeruginosa biofilm formation by impacting the pqs quorum sensing system

Pseudomonas aeruginosa is one of the leading nosocomial pathogens that causes both severe acute and chronic infections. The strong capacity of P. aeruginosa to form biofilms can dramatically increase its antibiotic resistance and lead to treatment failure. The biofilm resident bacterial cells display distinct gene expression profiles and phenotypes compared to their free-living counterparts. Elucidating the genetic determinants of biofilm formation is crucial for the development of antibiofilm drugs. In this study, a high-throughput transposon-insertion site sequencing (Tn-seq) approach was employed to identify novel P. aeruginosa biofilm genetic determinants. When analyzing the novel biofilm regulatory genes, we found that the cell division factor ZapE (PA4438) controls the P. aeruginosa pqs quorum sensing system. The ∆zapE mutant lost fitness against the wild-type PAO1 strain in biofilms and its production of 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS) had been reduced. Further biochemical analysis showed that ZapE interacts with PqsH, which encodes the synthase that converts 2-heptyl-4-quinolone (HHQ) to PQS. In addition, site-directed mutagenesis of the ATPase active site of ZapE (K72A) abolished the positive regulation of ZapE on PQS signaling. As ZapE is highly conserved among the Pseudomonas group, our study suggests that it is a potential drug target for the control of Pseudomonas infections.

Metabolomic insight into the synergistic mechanism of action of a bacterial consortium in plant growth promotion

It has been established that a consortium consisting of compatible plant growth promoting rhizobacterial strains outperforms their individual impacts on plant attributes. While the phenomenon of synergism is extensively reported, the mechanism that underpins it is yet to be elucidated. In the present study the impact of three plant growth promoting bacteria, Azotobacter chroococcum (A), Priestia megaterium (formerly Bacillus megaterium) (B), and Pseudomonas sp. SK3 (P) was studied as a consortium on the growth attributes of pigeonpea. In addition, microbe-microbe interactions were investigated through metabolomic profiling to understand the mechanism of synergism. Plant growth experiments revealed that bacterial consortium A + B + P showed a significant increase in plant attributes such as shoot length, root length, fresh weight, and dry weight as compared to monocultures and two-membered consortia. Metabolomic profiling through high resolution liquid chromatograph mass spectrometer revealed the presence of a few bioactive compounds in the consortium that might play a potential role in the enhancement of biometric parameters of the plant. Several compounds, such as antipyrine, 6,6-dimethoxy-2,5,5-trimethyl-2-hexene, N-methyltryptamine, 2,2-dimethyl-3,4-bis(4-methoxyphenyl)-2H-1-benzopyran-7-ol acetate, N6-hydroxy-l-lysine, and l-furosin, were detected in the metabolome of the consortium, which was unique among all the treatments. The study also detected a few metabolites involved in sphingolipid biosynthesis (ketosphinganine and sphinganine) known for cell signaling in the consortium. This unravels the possible mechanism of synergism between bacterial strains in a consortium. The metabolomic profile would be helpful to strategically develop unique and more effective consortia that are tailored to the soil type.

Exemplifying the next generation of antibiotic susceptibility intensifiers of phytochemicals by LasR-mediated quorum sensing inhibition

There persists a constant threat from multidrug resistance being acquired by all human pathogens that challenges the well-being of humans. This phenomenon is predominantly led by Pseudomonas aeruginosa which is already resistant to the current generations of antibiotic by altering its metabolic pathways to survive. Specifically for this microbe the phenomenon of quorum sensing (QS) plays a crucial role in acquiring virulence and pathogenicity. QS is simply the cross talk between the bacterial community driven by signals that bind to receptors, enabling the entire bacterial microcosm to function as a single unit which has led to control P. aeruginosa cumbersome even in presence of antibiotics. Inhibition of QS can, therefore, be of a significant importance to curb such virulent and pathogenic strains of P. aeruginosa. Natural compounds are well known for their antimicrobial properties, of which, information on their mode of action is scarce. There can be many antimicrobial phytochemicals that act by hindering QS-pathways. The rationale of the current study is to identify such natural compounds that can inhibit QS in P. aeruginosa driven by LasR, PhzR, and RhlR dependent pathways. To achieve this rationale, in silico studies were first performed to identify such natural compounds which were then validated by in vitro experiments. Gingerol and Curcumin were identified as QS-antagonists (QSA) which could further suppress the production of biofilm, EPS, pyocyanin, and rhamnolipid along with improving the susceptibility to antibiotics.

Mutation, Chemoprofiling, Dereplication, and Isolation of Natural Products from Penicillium oxalicum

Diethyl sulfate (DES)-based chemical mutagenesis was applied on different fungal strains with the aim of diversifying the secondary metabolites. The mutant strain (VRE-MT1) of Penicillium oxalicum was subjected to dereplication (LCMS-based) and isolation of natural products, resulting in obtaining 10 molecules of bioactive potential. Metabolites, viz. tuckolide, methylpenicinoline, 2-acetyl-3,5-dihydroxy-4,6-dimethylbenzeneacetic acid, penicillixanthone A, brefeldin A 7-ketone, and antibiotic FD 549, were observed for the first time from P. oxalicum. The results of antimicrobial activity reveal that the compounds N-[2-(4-hydroxyphenyl)ethenyl]formamide, methylpenicinoline, and penipanoid A have potent antibacterial activity against Bacillus subtilis (ATCC 6633) with minimum inhibitory concentration (MIC) values of 16, 64, and 16 μM, respectively, and the compounds N-[2-(4-hydroxyphenyl)ethenyl]formamide, methylpenicinoline, and penipanoid A were found active against Escherichia coli (ATCC 25922), with MIC values of 16, 64, and 16 μM, respectively. Also, the metabolites N-[2-(4-hydroxyphenyl)ethenyl]formamide and tuckolide showed effective antioxidant activity in 2,2-diphenyl-1-picrylhydrazyl and 2,2'-azino-bis(3-ethylbenzothiazoline)-6-sulfonic acid scavenging assays. The mutant VRE-MT1 was found to have 8.34 times higher quantity of N-[2-(4-hydroxyphenyl)ethenyl]formamide as compared to the mother strain. The DES-based mutagenesis strategy has been found to be a potent tool to diversify the secondary metabolites in fungi.

Biological and clinical significance of quorum sensing alkylquinolones: current analytical and bioanalytical methods for their quantification

Quorum sensing (QS) is a sophisticated bacterial communication system which plays a key role in the virulence and biofilm formation of many pathogens. The Pseudomonas aeruginosa QS network consists of four sets of connected systems (las, rlh, pqs and iqs) hierarchically organized. The pqs system involves characteristic autoinducers (AI), most of them sharing an alkylquinolone (AQ) structure, and is able to carry out several relevant biological functions besides its main signalling activity. Their role in bacterial physiology and pathogenicity has been widely studied. Indeed, the presence of these metabolites in several body fluids and infected tissues has pointed to their potential value as biomarkers of infection. In this review, we summarize the most recent findings about the biological implications and the clinical significance of the main P. aeruginosa AQs. These findings have encouraged the development of analytical and bioanalytical techniques addressed to assess the role of these metabolites in bacterial growth and survival, during pathogenesis or as biomarkers of infections. The availability of highly sensitive reliable analytical methods suitable for clinical analysis would allow getting knowledge about pathogenesis and disease prognosis or progression, supporting clinicians on the decision-making process for the management of these infections and guiding them on the application of more effective and appropriate treatments. The benefits from the implementation of the point-of-care (PoC)-type testing in infectious disease diagnostics, which are seen to improve patient outcomes by promoting earlier therapeutic interventions, are also discussed.

Multiplexed Signal Ion Emission Reactive Release Amplification (SIERRA) Assay for the Culture-Free Detection of Gram-Negative and Gram-Positive Bacteria and Antimicrobial Resistance Genes

The global prevalence of antibiotic-resistant bacteria has increased the risk of dangerous infections, requiring rapid diagnosis and treatment. The standard method for diagnosis of bacterial infections remains dependent on slow culture-based methods, carried out in central laboratories, not easily extensible to rapid identification of organisms, and thus not optimal for timely treatments at the point-of-care (POC). Here, we demonstrate rapid detection of bacteria by combining electrochemical immunoassays (EC-IA) for pathogen identification with confirmatory quantitative mass spectral immunoassays (MS-IA) based on signal ion emission reactive release amplification (SIERRA) nanoparticles with unique mass labels. This diagnostic method uses compatible reagents for all involved assays and standard fluidics for automatic sample preparation at POC. EC-IA, based on alkaline phosphatase-conjugated pathogen-specific antibodies, quantified down to 104 bacteria per sample when testing Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa lysates. EC-IA quantitation was also obtained for wound samples. The MS-IA using nanoparticles against S. aureus, E. coli, Klebsiella pneumoniae, and P. aeruginosa allowed selective quantitation of ∼105 bacteria per sample. This method preserves bacterial cells allowing extraction and amplification of 16S ribosomal RNA genes and antibiotic resistance genes, as was demonstrated through identification and quantitation of two strains of E. coli, resistant and nonresistant due to β-lactamase cefotaximase genes. Finally, the combined immunoassays were compared against culture using remnant deidentified patient urine samples. The sensitivities for these immunoassays were 83, 95, and 92% for the prediction of S. aureus, P. aeruginosa, and E. coli or K. pneumoniae positive culture, respectively, while specificities were 85, 92, and 97%. The diagnostic platform presented here with fluidics and combined immunoassays allows for pathogen isolation within 5 min and identification in as little as 15 min to 1 h, to help guide the decision for additional testing, optimally only on positive samples, such as multiplexed or resistance gene assays (6 h).

An Immunochemical Approach to Quantify and Assess the Potential Value of the Pseudomonas Quinolone Signal as a Biomarker of Infection

Quorum sensing (QS) is a bacterial cell density-based communication system using low molecular weight signals called autoinducers (AIs). Identification and quantification of these molecules could provide valuable information related to the stage of colonization or infection as well as the stage of the disease. With this scenario, we report here for the first time the development of antibodies against the PQS (pseudomonas quinolone signal), the main signaling molecule from the pqs QS system of Pseudomonas aeruginosa, and the development of a microplate-based enzyme-linked immunosorbent assay (ELISA) able of quantifying this molecule in complex biological media in the low nanometer range (LOD, 0.36 ± 0.14 nM in culture broth media). Moreover, the PQS ELISA here reported has been found to be robust and reliable, providing accurate results in culture media. The technique allowed us to follow up the PQS profile of the release of bacterial clinical isolates obtained from patients of different disease status. A clear correlation was found between the PQS immunoreactivity equivalents and the chronic or acute infection conditions, which supports the reported differences on virulence and behavior of these bacterial strains due to their adaptation capability to the host environment. The results obtained point to the potential of the PQS as a biomarker of infection and to the value of the antibodies and the technology developed for improving diagnosis and management of P. aeruginosa infections based on the precise identification of the pathogen, appropriate stratification of the patients according to their disease status, and knowledge of the disease progression.

Tailoring the cationic lipid composition of lipo-DVDMS augments the phototherapy efficiency of burn infection

Increase in infections with Gram-negative Pseudomonas aeruginosa (P. aeruginosa) is a serious global challenge in healthcare. Sinoporphyrin sodium (DVDMS) combined with photodynamic antimicrobial chemotherapy (PACT) can effectively eradicate Gram-positive organisms. However, the poor penetration of DVDMS into the Gram-negative bacterial cell membrane and bacterial biofilm greatly limits the photo-inspired antimicrobial activity. This study optimized the cationic lipid-mediated nano-DVDMS delivery to improve the cellular uptake, and evaluated the antimicrobial efficacy of cationic DVDMS-liposome (CDL)-provoked PACT in both P. aeruginosa and its multidrug resistant strain. The results showed that the positively charged liposome modification promoted the enrichment of DVDMS in Gram-negative bacteria. CDL-PACT-produced ROS and caused bacterial death, accompanied by the decreased expression levels of virulence factor-related genes. The P. aeruginosa-infected burn model indicated satisfactory bacterial eradication and accelerated wound healing after CDL-PACT, in addition to gradually increasing bFGF, VEGF, TGF-β₁ and Hyp levels and reducing TNF-α and IL-6, with no detectable side-effects. Overall, these findings provide fundamental knowledge that enables the design of feasible and efficient PACT treatments, including biophysical membrane permeabilization and photodynamic eradication, which are promising to overcome the infection and resistance of highly opportunistic Gram-negative bacteria.

Plant Beneficial Features and Application of Paraburkholderia sp. NhPBG1 Isolated from Pitcher of Nepenthes hamblack

Pitchers are the unique structures of carnivorous plants used for the trapping of insects and other small invertebrates. The digestion of captured prey here is assisted by the bacteria, which have been associated with pitchers. These bacterial communities can therefore expect to have a variety of plant beneficial functions. In this study, the bacterial isolate NhPBG1 from the pitcher of Nepenthes hamblack was screened for activity against Pythium aphanidermatum, Rhizoctonia solani, Fusarium oxysporum, and Colletotrichum accutatum and was found to have the inhibitory activity towards all the tested phytopathogens. Interestingly, the isolate was found to have hyper-inhibitory effect against P. aphanidermatum. Further to this, the isolate was also shown to be positive for plant beneficial traits such as indole-3-acetic acid (IAA) and ammonia production, phosphate, potassium and zinc solubilization, nitrogen fixation, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. BLAST analysis of the 16S rDNA sequence of NhPBG1 has identified it as Paraburkholderia sp. Also, the Zingiber officinale rhizome pre-treated with NhPBG1 was found to get protected from P. aphanidermatum induced infection, whereas the control showed symptoms of infection. This was further confirmed by the microscopic evaluation of the presence of fungal mycelia in the tissues of control. However, the mycelial invasion could not be detected in the NhPBG1 treated rhizome. The metabolite profiling of NhPBG1 by GC-MS has identified variety of general metabolites, while the antifungal compounds pyocyanin and 1-hydroxyphenazine could be identified by the LC-MS/MS analysis.

High-Throughput Immunochemical Method to Assess the 2-Heptyl-4-quinolone Quorum Sensing Molecule as a Potential Biomarker of Pseudomonas aeruginosa Infections

Bacterial quorum sensing (QS) is being contemplated as a promising target for developing innovative diagnostic and therapeutic strategies. Here we report for the first time the development of antibodies against 2-heptyl-4-quinolone (HHQ), a signaling molecule from the pqs QS system of Pseudomonas aeruginosa, involved in the production of important virulent factors and biofilm formation. The antibodies produced were used to develop an immunochemical diagnostic approach to assess the potential of this molecule as a biomarker of P. aeruginosa infection. The ELISA developed is able to reach a detectability in the low nM range (IC₅₀ = 4.59 ± 0.29 nM and LOD = 0.34 ± 0.13 nM), even in complex biological samples such as Müeller Hinton (MH) culture media. The ELISA developed is robust and reproducible and has been found to be specific to HHQ, with little interference from other related alkylquinolones from the pqs QS system. The ELISA has been used to analyze the HHQ production kinetics of P. aeruginosa clinical isolates grown in MH media, pointing to its potential as a biomarker of infection and at the possibility to use the technology developed to obtain additional information about the disease stage.